/usr/lib/R/site-library/Biobase/scripts/getBioC.R is in r-bioc-biobase 2.38.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 | # This function gets and installs the required Bioconductor libraries.
#
# libName: a vector of character string for the name of the library to be
# installed. Valid names include "all" - all the released packages,
# "affy" - packages "affy" plus exprs, "CDNA" - packages "CDNA" plus
# exprs, and "exprs" - packages "Biobase", "annotate", "genefilter",
# "geneploter", "edd", "Roc", and "tkWidgets".
# destdir: a character string for the directory where the downloaded
# packages will be stored.
# isDevel: a boolean indicating whether the released (FALSE) or
# developer (TRUE) version will be downloaded and installed.
# verbose: a boolean indicating whether any error related to the
# downloading process will be (TRUE) printed. Error messages will
# still be returned but invisible if berbose is set to FALSE.
# bundle: a boolean indicating whether packages will be downloaded as
# bundles (TRUE) or individual packages (FALSE). Valid bundle
# (e. g. "all", "exprs") or package ("tkWidgets", "annotate") have to
# be used in each case.
#
getBioC <- function (libName = "exprs", destdir = NULL, isDevel = FALSE,
verbose = TRUE, bundle = TRUE){
on.exit(options(show.error.messages = TRUE))
PLATFORM <- .Platform$OS.type
DESTDIR <- ifelse(is.null(destdir), getwd(), destdir)
messages <- NULL
packs <- NULL
if(bundle){
for(i in libName){
packs <- c(packs, getPackNames(i))
}
}else{
packs <- libName
}
repository <- getPkgDisc(isDevel)
for(i in packs){
sourceUrl <- getDLURL(i, repository, PLATFORM)
fileName <- getFileName(sourceUrl)
# check the connection instead of downloading directly which
# will write files of 0 size in the directory even when
# the connection is not there.
options(show.error.messages = FALSE)
tryMe <- try(url(sourceUrl, "r"))
options(show.error.messages = TRUE)
if(inherits(tryMe, "try-error")){
messages <- c(messages, paste("Get", i, "failed"))
}else{
close(tryMe)
download.file(sourceUrl, fileName,
mode = getMode(PLATFORM), quiet = TRUE)
options(show.error.messages = FALSE)
tryMe <- try(installPack(PLATFORM, fileName))
options(show.error.messages = TRUE)
if(inherits(tryMe, "try-error")){
messages <- c(messages,
paste("Install", i, "failed"))
}
}
}
if(is.null(messages))
messages <- "Download was successful"
if(verbose)
print(messages)
return(invisible(messages))
}
getPackNames <- function (libName){
error <- paste("The library is not valid. Must be:",
"all, exprs, affy, or CDNA", sep = "\n")
AFFY <- "affy"
CDNA <- c("marrayInput", "marrayClasses", "marrayNorm",
"marrayPlots")
EXPRS <-c("Biobase", "annotate", "genefilter", "geneplotter",
"edd", "ROC", "tkWidgets")
switch(libName,
"all" = return(c(EXPRS, AFFY, CDNA)),
"exprs" = return(EXPRS),
"affy" = return(c(EXPRS, AFFY)),
"cdna" =,
"CDNA" = return(c(EXPRS, CDNA)),
stop(error))
}
getMode <- function(platform){
switch(platform,
"unix" = return("w"),
"windows" = return("wb"),
stop("OS system not surported"))
}
installPack <- function(platform, fileName){
if(platform == "unix"){
system(paste("R CMD INSTALL ", fileName, sep = ""), TRUE)
}else{
if(platform == "windows"){
install.packages(fileName, .libPaths()[1], CRAN = NULL)
}else{
stop("The OS system is not supported")
}
}
}
getDLURL <- function(pakName, rep, platform){
sourceURL <- NULL
isPkg <- FALSE
version <- 0
higherV <- FALSE
for(i in rep){
if(gsub("^Package: *(.*)", "\\1", i) == pakName){
isPkg <- TRUE
}
if(isPkg && regexpr("^Version:", i)[1] > 0){
if(gsub("^Version: *(.*)", "\\1", i) > version)
higherV <- TRUE
else
higherV <- FALSE
}
if(platform == "windows"){
if(isPkg && higherV && regexpr("Win32URL", i)[1] > 0){
sourceURL <- gsub("^Win32URL: *(.*)", "\\1", i)
isPkg = FALSE
}
}else{
if(isPkg && higherV && regexpr("/Source/", i)[1] > 0){
sourceURL <- gsub("^SourceURL: *(.*)", "\\1", i)
isPkg <- FALSE
}
}
}
return(sourceURL)
}
getPkgDisc <- function (isDevel){
on.exit(options(show.error.messages = TRUE))
if(isDevel)
URL <-
"http://www.bioconductor.org/packages/devel/distrib/PACKAGES"
else
URL <-
"http://www.bioconductor.org/packages/release/distrib/PACKAGES"
con <- url(URL)
options(show.error.messages = FALSE)
tryMe <- try(readLines(con))
options(show.error.messages = TRUE)
if(inherits(tryMe, "try-error"))
stop("The url for BioC PACKAGES is incorrect")
close(con)
return(tryMe)
}
getFileName <- function(url){
temp <- unlist(strsplit(url, "/"))
return(temp[length(temp)])
}
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